when using the motifMatches() to scan the sequence in chromVAR , I awalys use JASPAR2016/JASPAR2018 to get the PFMatrix. But the number of motif in database is limited. And some motif I interested in is not in database. I am wondering whether I can use the MEME suite result like this
`
MEME version 4.4
ALPHABET= ACGT
strands: + -
Background letter frequencies (from file `../../promoter_background/Ath.bg'):
A 0.33230 C 0.16770 G 0.16770 T 0.33230
when using the motifMatches() to scan the sequence in chromVAR , I awalys use JASPAR2016/JASPAR2018 to get the PFMatrix. But the number of motif in database is limited. And some motif I interested in is not in database. I am wondering whether I can use the MEME suite result like this ` MEME version 4.4
ALPHABET= ACGT
strands: + -
Background letter frequencies (from file `../../promoter_background/Ath.bg'): A 0.33230 C 0.16770 G 0.16770 T 0.33230
MOTIF AT1G01060 MP00119
letter-probability matrix: alength= 4 w= 10 nsites= 599 E= 4.8e-803 0.854758 0.001669 0.051753 0.091820
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.996661 0.003339 0.000000 0.000000
0.000000 0.013356 0.008347 0.978297
0.005008 0.000000 0.005008 0.989983
0.085142 0.010017 0.000000 0.904841
0.287145 0.076795 0.056761 0.579299
0.188648 0.240401 0.195326 0.375626
URL http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=AT1G01060.1#bind_motif
`
If it support, the number of motif scaning the sequence is no longer restricted when I use ChromVAR to computeDeviations :）
Best Regard